Strain identifier

BacDive ID: 140534

Type strain: Yes

Species: Thioclava nitratireducens

Strain Designation: 25B10_4

NCBI tax ID(s): 1915078 (species)

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General

@ref: 43318

BacDive-ID: 140534

keywords: genome sequence, 16S sequence, Bacteria, aerobe, mesophilic, Gram-negative, motile, rod-shaped, colony-forming

description: Thioclava nitratireducens 25B10_4 is an aerobe, mesophilic, Gram-negative bacterium that forms circular colonies and was isolated from surface seawater of the Bering Sea.

NCBI tax id

  • NCBI tax id: 1915078
  • Matching level: species

doi: 10.13145/bacdive140534.20230509.8.1

Name and taxonomic classification

LPSN

  • @ref: 20215
  • description: domain/bacteria
  • keyword: phylum/pseudomonadota
  • domain: Bacteria
  • phylum: Pseudomonadota
  • class: Alphaproteobacteria
  • order: Rhodobacterales
  • family: Paracoccaceae
  • genus: Thioclava
  • species: Thioclava nitratireducens
  • full scientific name: Thioclava nitratireducens Liu et al. 2017

@ref: 43318

domain: Bacteria

phylum: Proteobacteria

class: Alphaproteobacteria

order: Rhodobacterales

family: Rhodobacteraceae

genus: Thioclava

species: Thioclava nitratireducens

strain designation: 25B10_4

type strain: yes

Morphology

cell morphology

@refgram staincell lengthcell widthcell shapemotilityflagellum arrangementconfidence
43318negative1.1-1.2 µm0.6-0.7 µmrod-shapedyespolar
69480negative99.999

colony morphology

  • @ref: 43318
  • colony size: 1-2 mm
  • colony color: cream
  • colony shape: circular
  • incubation period: 3 days
  • medium used: Marine agar 2216

Culture and growth conditions

culture medium

@refnamegrowth
43318Marine broth 2216yes
43318Marine agar (MA)yes
43318Motility agaryes

culture temp

@refgrowthtypetemperaturerange
43318positiveoptimum28mesophilic
43318positivegrowth10-43

culture pH

@refabilitytypepHPH range
43318positivegrowth6-9alkaliphile
43318positiveoptimum7

Physiology and metabolism

oxygen tolerance

  • @ref: 43318
  • oxygen tolerance: aerobe

spore formation

@refspore formationconfidence
69481no100
69480no99.993

halophily

@refsaltgrowthtested relationconcentration
43318NaClpositivegrowth0-12 %(w/v)
43318NaClpositiveoptimum3-4 %(w/v)

observation

  • @ref: 43318
  • observation: quinone Q-10

metabolite utilization

@refChebi-IDmetaboliteutilization activitykind of utilization tested
4331817632nitrate+reduction
4331817634D-glucose+fermentation
433184853esculin+hydrolysis
4331817634D-glucose+carbon source
4331830849L-arabinose+carbon source
4331816024D-mannose+carbon source
4331816899D-mannitol+carbon source
4331817306maltose+carbon source
4331832032potassium gluconate+carbon source
4331825115malate+carbon source
4331853258sodium citrate+carbon source
433185291gelatin-hydrolysis
43318506227N-acetylglucosamine-carbon source
4331827689decanoate-carbon source
4331817128adipate-carbon source
4331818401phenylacetate-carbon source
4331816947citrate+carbon source
4331817234glucose+builds acid from
4331829864mannitol-builds acid from
4331817268myo-inositol-builds acid from
4331830911sorbitol-builds acid from
4331826546rhamnose-builds acid from
4331817992sucrose-builds acid from
4331828053melibiose-builds acid from
4331827613amygdalin-builds acid from
4331822599arabinose-builds acid from

metabolite production

@refChebi-IDmetaboliteproduction
4331835581indoleno
4331816136hydrogen sulfideno
4331830854indole-3-acetateno
4331815688acetoinno

metabolite tests

  • @ref: 43318
  • Chebi-ID: 15688
  • metabolite: acetoin
  • voges-proskauer-test: -

enzymes

@refvalueactivityec
43318catalase+1.11.1.6
43318cytochrome oxidase+1.9.3.1
43318alkaline phosphatase+3.1.3.1
43318esterase (C 4)+
43318esterase Lipase (C 8)+
43318lipase (C 14)+
43318leucine arylamidase+3.4.11.1
43318valine arylamidase+
43318acid phosphatase+3.1.3.2
43318naphthol-AS-BI-phosphohydrolase+
43318alpha-galactosidase+3.2.1.22
43318alpha-glucosidase+3.2.1.20
43318cystine arylamidase-3.4.11.3
43318trypsin-3.4.21.4
43318alpha-chymotrypsin-3.4.21.1
43318beta-glucuronidase-3.2.1.31
43318N-acetyl-beta-glucosaminidase-3.2.1.52
43318alpha-mannosidase-3.2.1.24
43318alpha-fucosidase-3.2.1.51
43318beta-glucosidase+3.2.1.21
43318beta-galactosidase+3.2.1.23
43318urease+3.5.1.5
43318arginine dihydrolase-3.5.3.6
43318lysine decarboxylase-4.1.1.18
43318tryptophan deaminase-4.1.99.1
43318gelatinase-

fatty acid profile

  • fatty acids

    @reffatty acidpercentage
    43318C11:00.2
    43318C16:01.8
    43318C17:00.3
    43318C18:02.4
    43318C16:0 iso0.1
    43318C11:0 iso 3OH0.1
    43318C10:0 3OH4.3
    43318C12:0 3OH0.1
    43318C16:0 3OH0.2
    43318C17:0 3OH0.1
    43318C17:0 cyclo0.2
    43318C17:1ω7c0.4
    43318C18:1ω7c 11-methyl1.4
    43318C19:0 10-methyl1.5
    43318C19:0 cyclo ω8c1.8
    43318C14:0 3OH / C16:1 iso I0.1
    43318C16:1ω7c / C16:1ω6c2.3
    43318Unknown 18.846 / C19:1ω6c0.2
    43318C18:1ω7c / C18:1ω6c82.3
  • type of FA analysis: whole cell analysis
  • incubation medium: Marine agar 2216
  • agar/liquid: agar
  • incubation temperature: 28
  • software version: Sherlock 6.0B
  • system: MIS MIDI
  • instrument: Agilent 6850 gas chromatograph
  • cutoff value:

Isolation, sampling and environmental information

isolation

  • @ref: 43318
  • sample type: surface seawater of the Bering Sea
  • geographic location: Bering Sea
  • latitude: 59
  • longitude: 179

isolation source categories

Cat1Cat2Cat3
#Environmental#Aquatic#Marine
#Environmental#Aquatic#Surface water

taxonmaps

  • @ref: 69479
  • File name: preview.99_1484.png
  • url: https://microbeatlas.org/index.html?action=taxon&taxon_id=90_19;96_849;97_991;98_1170;99_1484&stattab=map
  • Last taxonomy: Thioclava
  • 16S sequence: KX618935
  • Sequence Identity:
  • Total samples: 2098
  • soil counts: 226
  • aquatic counts: 1428
  • animal counts: 413
  • plant counts: 31

Sequence information

16S sequences

  • @ref: 43318
  • description: 16S rRNA gene sequence
  • accession: KX618935
  • database: nuccore

Genome sequences

@refdescriptionaccessionassembly leveldatabaseNCBI tax ID
66792Thioclava nitratireducens 25B10_4GCA_001940525completencbi1915078
66792Thioclava nitratireducens 25B10_42751185746completeimg1915078

GC content

  • @ref: 43318
  • GC-content: 63.8
  • method: genome sequence analysis

Genome-based predictions

predictions

traitpredictionconfidencetraining_data
spore-formingno100no
flagellatedno78.618no
flagellatedno78.618no
gram-positiveno98.409no
gram-positiveno98.409no
anaerobicno97.039no
anaerobicno97.039no
halophileyes53.575no
halophileyes53.575no
spore-formingno96.364no
spore-formingno96.364no
glucose-utilyes84.462yes
glucose-utilyes84.462yes
aerobicyes82.296yes
aerobicyes82.296yes
thermophileno96.63yes
thermophileno96.63yes
motileyes57.092yes
motileyes57.092yes
glucose-fermentno91.455no
glucose-fermentno91.455no

External links

@ref: 43318

culture collection no.: MCCC 1A07302, LMG 29614

literature

  • topic: Phylogeny
  • Pubmed-ID: 28598317
  • title: Thioclava nitratireducens sp. nov., isolated from surface seawater.
  • authors: Liu Y, Lai Q, Shao Z
  • journal: Int J Syst Evol Microbiol
  • DOI: 10.1099/ijsem.0.001844
  • year: 2017
  • mesh: Arctic Regions, Bacterial Typing Techniques, Base Composition, DNA, Bacterial/genetics, Fatty Acids/chemistry, Glycolipids/chemistry, Nucleic Acid Hybridization, Phospholipids/chemistry, *Phylogeny, RNA, Ribosomal, 16S/genetics, Rhodobacteraceae/*classification/genetics/isolation & purification, Seawater/*microbiology, Sequence Analysis, DNA, Ubiquinone/chemistry
  • topic2: Transcriptome

Reference

@idauthorstitledoi/urljournalpubmed
20215Parte, A.C., Sardà Carbasse, J., Meier-Kolthoff, J.P., Reimer, L.C. and Göker, M.List of Prokaryotic names with Standing in Nomenclature (LPSN) moves to the DSMZ10.1099/ijsem.0.004332
43318Yang Liu, Qiliang Lai, Zongze ShaoThioclava nitratireducens sp. nov., isolated from surface seawater10.1099/ijsem.0.001844IJSEM 67: 2109-2113 201728598317
66792Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannAutomatically annotated for the DiASPora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69479João F Matias Rodrigues, Janko Tackmann,Gregor Rot, Thomas SB Schmidt, Lukas Malfertheiner, Mihai Danaila,Marija Dmitrijeva, Daniela Gaio, Nicolas Näpflin and Christian von Mering. University of Zurich.MicrobeAtlas 1.0 betahttps://microbeatlas.org/
69480Julia Koblitz, Joaquim Sardà, Lorenz Christian Reimer, Boyke Bunk, Jörg OvermannPredictions based on genome sequence made in the Diaspora project (Digital Approaches for the Synthesis of Poorly Accessible Biodiversity Information)https://diaspora-project.de/progress.html#genomes
69481Xiao-Yin To, René Mreches, Martin Binder, Alice C. McHardy, Philipp C. MünchPredictions based on the model GenomeNet Sporulation v. 110.21203/rs.3.rs-2527258/v1